ArticleGenome research2014
Canonical nucleosome organization at promoters forms during genome activation.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
- A comparative analysis of promoter-proximal pausing reveals kinetic and distributional dimensions of variation.bioRxiv : the preprint server for biology · 2026Article
- RNA Pol I shapes meiotic chromatin, germline H3K4me3 dynamics, and oogenesis independent of ribosome assembly.Cell reports · 2026Article
- Local nuclear to cytoplasmic ratio regulates H3.3 incorporation via cell cycle state during zygotic genome activation.EMBO reports · 2025Article
- RNA Pol I activity is required for meiotic chromatin organization and the H3K4me3 gradient essential for oogenesis, independent of ribosome synthesis.bioRxiv : the preprint server for biology · 2025Article
- H3K4me2 distinguishes a distinct class of enhancers during the maternal-to-zygotic transition.PLoS biology · 2025Article
- Coordinated action of multiple active histone modifications shapes the zygotic genome activation in teleost embryos.Nature communications · 2025Article
- Screening of functional maternal-specific chromatin regulators in early embryonic development of zebrafish.Communications biology · 2024Article
- The developmental and evolutionary characteristics of transcription factor binding site clustered regions based on an explainable machine learning model.Nucleic acids research · 2024Article
- Chromatin conformation and histone modification profiling across human kidney anatomic regions.Scientific data · 2024Article
- PGEProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Epigenomic dynamics of early Xenopus Embryos.Development, growth & differentiation · 2022Review
- Dynamic nucleosome organization after fertilization reveals regulatory factors for mouse zygotic genome activation.Cell research · 2022Article
- Aberrant nucleosome organization in mouse SCNT embryos revealed by ULI-MNase-seq.Stem cell reports · 2022Article
- Epigenetic Reprogramming in Early Animal Development.Cold Spring Harbor perspectives in biology · 2022Review
- The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation.Molecular cell · 2022Article
- Article
- Temporal Dynamic Analysis of Alternative Splicing During Embryonic Development in Zebrafish.Frontiers in cell and developmental biology · 2022Article
- RNA polymerase II clusters form in line with surface condensation on regulatory chromatin.Molecular systems biology · 2021Article
- Antisense RNAs during early vertebrate development are divided in groups with distinct features.Genome research · 2021Article
- Control of zygotic genome activation in Xenopus.Current topics in developmental biology · 2021Review
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10 authors.
Funding
Abstract
The organization of nucleosomes influences transcriptional activity by controlling accessibility of DNA binding proteins to the genome. Genome-wide nucleosome binding profiles have identified a canonical nucleosome organization at gene promoters, where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. The mechanisms of formation and the function of canonical promoter nucleosome organization remain unclear. Here we analyze the genome-wide location of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear on thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization is independent of DNA sequence preference, transcriptional elongation, and robust RNA polymerase II (Pol II) binding. Instead, canonical promoter nucleosome organization correlates with the presence of histone H3 lysine 4 trimethylation (H3K4me3) and affects future transcriptional activation. These findings reveal that genome activation is central to the organization of nucleosome arrays during early embryogenesis.
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